def GenomeDISCO_wrapper(outdir,parameters,concise_analysis,samplename1,samplename2,chromo,running_mode,f1,f2,nodefile):
script_comparison_file=outdir+'/scripts/GenomeDISCO/'+samplename1+'.'+samplename2+'/'+chromo+'.'+samplename1+'.'+samplename2+'.sh'
subp.check_output(['bash','-c','mkdir -p '+os.path.dirname(script_comparison_file)])
script_comparison=open(script_comparison_file,'w')
script_comparison.write("#!/bin/sh"+'\n')
script_comparison.write('. '+bashrc_file+'\n')
if os.path.isfile(f1) and os.path.getsize(f1)>20:
if os.path.isfile(f2) and os.path.getsize(f2)>20:
concise_analysis_text=''
if concise_analysis:
concise_analysis_text=' --concise_analysis'
#get the sample that goes for subsampling
subsampling=parameters['GenomeDISCO']['subsampling']
if parameters['GenomeDISCO']['subsampling']!='NA' and parameters['GenomeDISCO']['subsampling']!='lowest':
subsampling_sample=parameters['GenomeDISCO']['subsampling']
subsampling=outdir+'/data/edges/'+subsampling_sample+'/'+subsampling_sample+'.'+chromo+'.gz'
outpath=outdir+'/results/reproducibility/'+samplename1+'.vs.'+samplename2+'/GenomeDISCO/'
subp.check_output(['bash','-c','mkdir -p '+outpath])
script_comparison.write("$mypython -W ignore "+os.path.abspath(os.path.dirname(os.path.dirname(os.path.realpath(__file__)))+"/genomedisco/compute_reproducibility.py")+" --m1 "+f1+" --m2 "+f2+" --m1name "+samplename1+" --m2name "+samplename2+" --node_file "+nodefile+" --outdir "+outpath+" --outpref "+chromo+" --m_subsample "+subsampling+" --approximation 10000000 --norm "+parameters['GenomeDISCO']['norm']+" --method RandomWalks "+" --tmin "+parameters['GenomeDISCO']['tmin']+" --tmax "+parameters['GenomeDISCO']['tmax']+concise_analysis_text+'\n')
script_comparison.close()
run_script(script_comparison_file,running_mode)
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